The Repeatome in the Mega-Genus Epidendrum L. (Epidendroideae, Orchidaceae): An In Silico Comparative Analysis

The repeatome is composed of satellite DNA (satDNA) and transposable elements (TEs), and variation in its composition is important for shaping genome architecture and driving evolutionary processes in plants. As no repeatome assessment exists for Epidendrum, the largest genus of Orchidaceae in the Neotropics, we aim to describe repetitive sequences across its species. We performed phylogenetic analyses based on plastid (matK and rbcL) and nuclear (ITS) markers using maximum likelihood and Bayesian inference methods, and characterized the repeatome of 34 species using the RepeatExplorer2 pipeline. Our results reveal substantial variation in satDNA content among species, with a total of 208 individually identified satDNAs, which were used to build a custom database for repeatome comparative analysis. We found that 73 satDNA clusters are shared among species, while only three are species-specific (CL359 and CL82 in E. rigidum, and CL430 in E. gasteriferum), supporting the library hypothesis. Regarding TEs, Class I elements were the most abundant repeats identified in Epidendrum, primarily long terminal repeat retrotransposons of the Ty3-gypsy superfamily. Elements of the Ty1-copia superfamily were the least abundant. Only two Class II TIR superfamilies were identified, namely EnSpm_CACTA and hAT. The heterogeneous distribution of satDNAs and TEs among closely related species suggests lineage-specific patterns of expansion and contraction, potentially influenced by evolutionary processes such as hybridization and environmental adaptation. Our findings represent the first comprehensive characterization of the repeatome in Epidendrum and provide a basis for future studies on the composition and cytogenomic variation within the mega-genus.